Enhancements to enable paramamonster to be used via accessible/published visualizations. Pack scripts.

lib/galaxy/web/controllers/tracks.py

@@ -470,8 +470,10 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
         return self.tracks_grid( trans, **kwargs )
                     
     @web.expose
-    @web.require_login( "use Galaxy visualizations", use_panels=True )
     def paramamonster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ):
+        # Need to create history if necessary in order to create tool form.
+        trans.get_history( create=True )
+
         if id:
             # Loading a shared visualization.
             viz = self.get_visualization( trans, id )
@@ -495,7 +497,6 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
         return trans.fill_template_mako( "visualization/paramamonster.mako", config=viz_config )
     
     @web.expose
-    @web.require_login( "use Galaxy visualizations", use_panels=True )
     def circster( self, trans, hda_ldda, dataset_id ):
         # Get dataset.
         dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )

static/scripts/packed/mvc/data.js

@@ -0,0 +1 @@
+var Dataset=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda"}});var DatasetCollection=Backbone.Collection.extend({model:Dataset});

static/scripts/packed/mvc/ui.js

@@ -1 +1 @@
-var create_icon_buttons_menu=function(a){var b=new IconButtonCollection(_.map(a,function(c){return new IconButton(c)}));return new IconButtonMenuView({collection:b})};var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});
+var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tipsy_config:{}}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tipsy_config){b.tipsy(c.attributes.tipsy_config)}});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});

static/scripts/packed/viz/trackster_ui.js

@@ -1 +1 @@
-var add_bookmark=function(d,b){var f=$("#bookmarks-container"),h=$("<div/>").addClass("bookmark").appendTo(f),g=$("<div/>").addClass("delete-icon-container").appendTo(h).click(function(){h.slideUp("fast");h.remove();view.has_changes=true;return false}),a=$("<a href=''/>").addClass("icon-button delete").appendTo(g),i=$("<div/>").addClass("position").appendTo(h),e=$("<a href=''/>").text(d).appendTo(i).click(function(){view.go_to(d);return false}),c=$("<div/>").text(b).make_text_editable({num_rows:3,use_textarea:true,help_text:"Set bookmark note"}).addClass("annotation").appendTo(h);view.has_changes=true;return h};var object_from_template=function(b,a){if("copy" in b){return b.copy(a)}else{var c=b.obj_type;if(!c){c=b.track_type}return new addable_objects[c](view,a,b)}};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(c,a,b,d){view=new View(c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var n=a.chrom,e=a.start,k=a.end,g=a.overview;if(n&&(e!==undefined)&&k){view.change_chrom(n,e,k)}}if(b){var h,f,j;for(var l=0;l<b.length;l++){view.add_drawable(object_from_template(b[l],view))}}view.update_intro_div();var o;for(var l=0;l<view.drawables.length;l++){if(view.drawables[l].name===g){view.set_overview(view.drawables[l]);break}}if(d){var m;for(var l=0;l<d.length;l++){m=d[l];add_bookmark(m.position,m.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
+var add_bookmark=function(d,b){var f=$("#bookmarks-container"),h=$("<div/>").addClass("bookmark").appendTo(f),g=$("<div/>").addClass("delete-icon-container").appendTo(h).click(function(){h.slideUp("fast");h.remove();view.has_changes=true;return false}),a=$("<a href=''/>").addClass("icon-button delete").appendTo(g),i=$("<div/>").addClass("position").appendTo(h),e=$("<a href=''/>").text(d).appendTo(i).click(function(){view.go_to(d);return false}),c=$("<div/>").text(b).make_text_editable({num_rows:3,use_textarea:true,help_text:"Set bookmark note"}).addClass("annotation").appendTo(h);view.has_changes=true;return h};var object_from_template=function(c,b,a){if("copy" in c){return c.copy(a)}else{var d=c.obj_type;if(!d){d=c.track_type}return new addable_objects[d](b,a,c)}};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(c,a,b,d){view=new View(c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var n=a.chrom,e=a.start,k=a.end,g=a.overview;if(n&&(e!==undefined)&&k){view.change_chrom(n,e,k)}}if(b){var h,f,j;for(var l=0;l<b.length;l++){view.add_drawable(object_from_template(b[l],view,view))}}view.update_intro_div();var o;for(var l=0;l<view.drawables.length;l++){if(view.drawables[l].name===g){view.set_overview(view.drawables[l]);break}}if(d){var m;for(var l=0;l<d.length;l++){m=d[l];add_bookmark(m.position,m.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};

static/scripts/viz/trackster.js

@@ -3054,8 +3054,6 @@ extend(Track.prototype, Drawable.prototype, {
                                 return new GenomeRegion({from_str: $(elt).children(".position").text()});
                             });
 
-                        console.log(regions_to_use);
-
                         // Get regions for visualization.
                         if (regions_to_use === 'cur') {
                             // Use only current region.

templates/base_panels.mako

@@ -54,11 +54,12 @@
             root_path: '${h.url_for( "/" )}',
             image_path: '${h.url_for( "/static/images" )}',
             tool_url: '${h.url_for( controller="/api/tools" )}',
-            data_url: '${h.url_for( controller="tracks", action="data" )}',
-            raw_data_url: '${h.url_for( controller="tracks", action="raw_data" )}',
-            converted_datasets_state_url: '${h.url_for( controller="tracks", action="converted_datasets_state" )}',
-            dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}',
-            visualization_url: '${h.url_for( controller="visualization", action="save" )}'
+            data_url: '${h.url_for( controller="/tracks", action="data" )}',
+            raw_data_url: '${h.url_for( controller="/tracks", action="raw_data" )}',
+            converted_datasets_state_url: '${h.url_for( controller="/tracks", action="converted_datasets_state" )}',
+            dataset_state_url: '${h.url_for( controller="/tracks", action="dataset_state" )}',
+            visualization_url: '${h.url_for( controller="/visualization", action="save" )}',
+            paramamonster_url: '${h.url_for( controller="/tracks", action="paramamonster" )}'
         });
     </script>
 </%def>

templates/display_base.mako

@@ -32,9 +32,9 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "jquery.rating", "autocomplete_tagging", 
-            "viz/trackster", "viz/trackster_ui", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "jquery.ui.sortable.slider", 
-            "farbtastic" )}
+    ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "jquery.rating", 
+            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "jquery.event.drag", "jquery.mousewheel", 
+            "jquery.autocomplete", "jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
         

templates/tracks/browser.mako

@@ -49,8 +49,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
     // Place URLs here so that url_for can be used to generate them.
     //
     galaxy_paths.set({
-        visualization_url: "${h.url_for( action='save' )}",
-        paramamonster_url: "${h.url_for( action='paramamonster' )}",
+        visualization_url: "${h.url_for( action='save' )}"
     });
     var 
         add_track_async_url = "${h.url_for( action='add_track_async' )}",